ArticleJournal of experimental botany2014
An expression quantitative trait loci-guided co-expression analysis for constructing regulatory network using a rice recombinant inbred line population.
Article in Journal of experimental botany, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
- Enhancing genomic prediction accuracy in Huaxi cattle through integration of transcriptomic data and a self-attention-based SNP selection strategy.BMC bioinformatics · 2026Article
- Integrative transcriptogenomic analyses reveal the regulatory network underlying rice eating and cooking quality and identify a role for alpha-globulin in modulating starch and sucrose metabolism.Plant communications · 2025Article
- Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits.Nature communications · 2024Article
- Integrated eQTL mapping approach reveals genomic regions regulating candidate genes of theFrontiers in plant science · 2024Article
- Expression Quantitative Trait Locus of Wood Formation-Related Genes inInternational journal of molecular sciences · 2023Article
- Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice.Rice (New York, N.Y.) · 2023Article
- Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks.Nature communications · 2023Article
- Co-expression network analysis reveals PbTGA4 and PbAPRR2 as core transcription factors of drought response in an important timber speciesFrontiers in plant science · 2023Article
- Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus.Genome biology · 2022Article
- Expressed genes and their new alleles identification during fibre elongation reveal the genetic factors underlying improvements of fibre length in cotton.Plant biotechnology journal · 2022Article
- Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition.International journal of molecular sciences · 2022Article
- Target-oriented prioritization: targeted selection strategy by integrating organismal and molecular traits through predictive analytics in breeding.Genome biology · 2022Article
- Gene regulation network analyses of pistil development in papaya.BMC genomics · 2022Article
- A consensus map for quality traits in durum wheat based on genome-wide association studies and detection of ortho-meta QTL across cereal species.Frontiers in genetics · 2022Article
- Genomic Basis of Transcriptome Dynamics in Rice under Field Conditions.Plant & cell physiology · 2021Article
- A statistical framework for QTL hotspot detection.G3 (Bethesda, Md.) · 2021Article
- Incorporation of parental phenotypic data into multi-omic models improves prediction of yield-related traits in hybrid rice.Plant biotechnology journal · 2021Article
- Detecting selection with a genetic cross.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Genome-wide expression quantitative trait locus analysis in a recombinant inbred line population for trait dissection in peanut.Plant biotechnology journal · 2020Article
- The Role of Transcriptional Regulation in Hybrid Vigor.Frontiers in plant science · 2020Review
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8 authors.
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Abstract
The ability to reveal the regulatory architecture of genes at the whole-genome level by constructing a regulatory network is critical for understanding the biological processes and developmental programmes of organisms. Here, we conducted an eQTL-guided function-related co-expression analysis to identify the putative regulators and construct gene regulatory network. We performed an eQTL analysis of 210 recombinant inbred lines (RILs) derived from a cross between two indica rice lines, Zhenshan 97 and Minghui 63, the parents of an elite hybrid, using data obtained by hybridizing RNA samples of flag leaves at the heading stage with Affymetrix whole-genome arrays. Making use of an ultrahigh-density single-nucleotide polymorphism bin map constructed by population sequencing, 13 647 eQTLs for 10 725 e-traits were detected, comprising 5079 cis-eQTLs (37.2%) and 8568 trans-eQTLs (62.8%). The analysis revealed 138 trans-eQTLs hotspots, each of which apparently regulates the expression variations of many genes. Co-expression analysis of functionally related genes within the framework of regulator-target relationships outlined by the eQTLs led to the identification of putative regulators in the system. The usefulness of the strategy was demonstrated with the genes known to be involved in flowering. We also applied this strategy to the analysis of QTLs for yield traits, which also suggested likely candidate genes. eQTL-guided co-expression analysis may provide a promising solution for outlining a framework for the complex regulatory network of an organism.
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